Population genetics of the nomenspecies Enterobacter cloacae

Rapid identification of Enterobacter hormaechei and Enterobacter cloacae genetic cluster III

AIM

Enterobacter cloacae complex bacteria are of both clinical and environmental importance. Phenotypic methods are unable to distinguish between some of the species in this complex, which often renders their identification incomplete. The goal of this study was to develop molecular assays to identify Enterobacter hormaechei and Ent. cloacae genetic cluster III which are relatively frequently encountered in clinical material.

METHODS AND RESULTS

The molecular assays developed in this study are qPCR technology based and served to identify both Ent. hormaechei and Ent. cloacae genetic cluster III. qPCR results were compared to hsp60 sequence analysis. Most clinical isolates were assigned to Ent. hormaechei subsp. steigerwaltii and Ent. cloacae genetic cluster III. The latter was proportionately more frequently isolated from bloodstream infections than from other material (P < 0·05).

CONCLUSION

The qPCR assays detecting Ent. hormaechei and Ent. cloacae genetic cluster III demonstrated high sensitivity and specificity.

SIGNIFICANCE AND IMPACT OF THE STUDY

The presented qPCR assays allow accurate and rapid identification of clinical isolates of the Ent. cloacae complex. The improved identifications obtained can specifically assist analysis of Ent. hormaechei and Ent. cloacae genetic cluster III in nosocomial outbreaks and can promote rapid environmental monitoring. An association was observed between Ent. cloacae cluster III and systemic infection that deserves further attention.

Reversible oxygen-tolerant hydrogenase carried by free-living N2-fixing bacteria isolated from the rhizospheres of rice, maize, and wheat

Hydrogen production by microorganisms is often described as a promising sustainable and clean energy source, but still faces several obstacles, which prevent practical application. Among them, oxygen sensitivity of hydrogenases represents one of the major limitations hampering the biotechnological implementation of photobiological production processes. Here, we describe a hierarchical biodiversity-based approach, including a chemochromic screening of hydrogenase activity of hundreds of bacterial strains collected from several ecosystems, followed by mass spectrometry measurements of hydrogenase activity of a selection of the H₂-oxidizing bacterial strains identified during the screen. In all, 131 of 1266 strains, isolated from cereal rhizospheres and basins containing irradiating waste, were scored as H₂-oxidizing bacteria, including Pseudomonas sp., Serratia sp., Stenotrophomonas sp., Enterobacter sp., Rahnella sp., Burkholderia sp., and Ralstonia sp. isolates. Four free-living N₂-fixing bacteria harbored a high and oxygen-tolerant hydrogenase activity, which was not fully inhibited within entire cells up to 150–250 μmol/L O₂ concentration or within soluble protein extracts up to 25–30 μmol/L. The only hydrogenase-related genes that we could reveal in these strains were of the hyc type (subunits of formate hydrogenlyase complex). The four free-living N₂-fixing bacteria were closely related to Enterobacter radicincitans based on the sequences of four genes (16S rRNA, rpoB, hsp60, and hycE genes). These results should bring interesting prospects for microbial biohydrogen production and might have ecophysiological significance for bacterial adaptation to the oxic–anoxic interfaces in the rhizosphere.

Subtractive hybridization yields a silver resistance determinant unique to nosocomial pathogens in the Enterobacter cloacae complex

The heterogeneity and the increasing clinical importance of the Enterobacter cloacae complex have often been discussed. However, little is known about molecular factors causing pathogenicity within this nomenspecies. Here, we analyzed the genetic differences between an avirulent plant isolate and a pathogenic strain causing an outbreak with septicemia in three patients. We identified an IncHI-2 plasmid as a major difference between these two strains. Besides resistance to several antibiotics, this plasmid encoded a silver resistance determinant. We further showed that this sil determinant was present not only in the analyzed outbreak strain but also in the vast majority of clinical isolates of the E. cloacae complex, predominantly in (sub)species that frequently cause nosocomial infections. The identified sil determinant was highly conserved within the E. cloacae complex and mediated resistance to up to 600 μM silver nitrate. As silver is often used as a disinfectant and treatment for burn wounds, we present here an important fitness factor within the clinically most prevalent subspecies of the E. cloacae complex. This provides a possible explanation for their unequal involvement in nosocomial and especially burn wound infections.

Prevalences of the Enterobacter cloacae complex and its phylogenetic derivatives in the nosocomial environment

Despite the importance of the Enterobacter cloacae complex as a nosocomial pathogen, little is known about the relative contribution of its single species and genotypes to its pathogenicity. We studied here the relationship between phylogenetically related strains and clinical infection sites. A total of 196 prospectively collected isolates of the E. cloacae complex were included in the study, comprising 67 blood culture isolates. Isolates were analyzed for clonality by pulsed-field gel electrophoresis (PFGE) and genetically assigned to their genotypes by partial hsp60 sequencing. Most isolates belonged in phylogenetic clade 1, with E. hormaechei being the most prevalent species. Notably, some genotypes and species, indeed, showed predilections to certain clinical specimens, whereas clinical outbreaks with members of the E. cloacae complex were rare. Our study stresses the need to identify alleged E. cloacae isolates on the subspecies level in clinical routine in order to obtain more insight into their distinct infectious potentials.

Matrix-assisted laser desorption and ionization-time-of-flight mass spectrometry, 16S rRNA gene sequencing, and API 32E for identification of Cronobacter spp.: a comparative study

Twenty-two isolates of the family Enterobacteriaceae, with focus on Cronobacter isolated from infant formula and the environment of milk powder plants, were comparatively identified using API 32E (bioMérieux, Marcy l'Etoile, France), 16S rRNA gene sequencing (Accugenix, Newark, USA), and matrix-assisted laser desorption and ionization-time-of-flight mass spectrometry (MALDI-TOF MS; Mabritec, Riehen, Switzerland and AnagnosTec, Potsdam, Germany). With API 32E, 22% of the isolates were assigned to species, 64% were assigned to a genus, and 14% could not be discriminated at any taxonomic level. Both 16S rRNA gene sequencing and MALDI-TOF MS assigned 100% of the isolates to species, but the identifications based on MALDI-TOF MS results were more discriminating and unequivocal. Our data indicate that MALDI-TOF MS provides the most rapid and unambiguous identification of Cronobacter and closely related Enterobacteriaceae isolates.

Outbreak of a novel Enterobacter sp. carrying blaCTX-M-15 in a neonatal unit of a tertiary care hospital in Tanzania

Enterobacter hormaechei and Cronobacter sakazakii are amongst the most important causes of outbreaks of neonatal sepsis associated with powdered milk. In this study, we report for the first time an outbreak of a novel Enterobacter sp. harbouring bla(CTX-M-15) in a neonatal unit in Tanzania. Seventeen Gram-negative enteric isolates from neonatal blood cultures were studied. Antibiotic susceptibility was assessed by disc diffusion testing, and the presence of the bla(CTX-M-15) gene was established by polymerase chain reaction (PCR) and sequencing. Isolates were typed by pulsed-field gel electrophoresis (PFGE). Identification by biochemical profiling was followed by nucleotide sequencing of 16S ribosomal DNA (rDNA), rpoB and hsp60 alleles. Environmental sampling was done and control measures were established. Isolates were initially misidentified based on their fermentation characteristics and agglutination as Salmonella enterica serotype Paratyphi. All isolates were resistant to multiple antibiotics, except for ciprofloxacin and carbapenems, and were found to harbour bla(CTX-M-15) on a 291-kb narrow-range plasmid. PFGE analysis indicated the clonal outbreak of a single strain, infecting 17 neonates with a case fatality rate of 35%. The same strain was isolated from a milk bucket. Phylogenetic analysis using 16S rDNA, rpoB and hsp60 sequences permitted no definitive identification, clustering the strains in the Enterobacter cloacae complex with similarities of 92-98.8%. The data describe an outbreak of a novel bla(CTX-M-15)-positive, multiresistant Enterobacter strain in an African neonatal unit that can easily be misidentified taxonomically. These data highlight the need for constant surveillance of bacteria harbouring extended-spectrum β-lactamases as well as improvements in hygiene measures in developing countries.

Resistance patterns and integron cassette arrays of Enterobacter cloacae complex strains of human origin

The aim of this research was to analyse the resistance patterns and characterize the distribution and genetic content of resistance integrons within Enterobacter cloacae complex strains originating from hospitalized patients. The strains were included in the E. cloacae complex study following sequence analysis of the hsp60 gene. The determination of resistance towards eight classes of antimicrobials was followed by PCR detection of integrons and analyses of the size and sequences of their variable parts. The majority of 69 clinical strains of the E. cloacae complex were identified as Enterobacter hormaechei. They were isolated from a variety of samples, including urine, wounds, blood and stools. The remaining isolates belonged to E. cloacae clusters III and IV, E. cloacae subsp. cloacae and Enterobacter kobei. Fifty-two isolates (75.4 %) were resistant to more than three unrelated antibiotics. The resistance for each antibiotic, except imipenem, was significantly associated with the presence of integrons. Class 1 integrons were detected in 55 % of isolates: 63.3 % of 'E. hormaechei subsp. steigerwaltii', 50 % of E. cloacae cluster III, 40 % of 'E. hormaechei subsp. oharae', 33 % belonging to E. cloacae cluster IV and 20 % of 'E. hormaechei subsp. hormaechei' were intI1-positive. All of the integrons were located on transferable genetic elements. The transferred resistance primarily included that to aminoglycosides, ticarcillin, piperacillin, sulfamethoxazole, trimethoprim and tetracycline. Sequence analysis of the variable regions of integrons identified two groups of genes: those encoding aminoglycoside adenylotransferases responsible for resistance to aminoglycosides, and dfr cassettes conferring resistance to trimethoprim. Integrons of the E. cloacae complex showed limited variability of genes encoding resistance to therapeutics and were stable in structure with the following cassette arrays: dfrA12-orfF-aadA2, aadB-aadA2, dfrA1-aadA1 and aacA4-aadA1. Hospital-dependent differences in type and arrays of gene cassettes were observed, which seemed to be conserved and not liable to changes.

Enterobacter mori sp. nov., associated with bacterial wilt on Morus alba L

Two isolates of mulberry-pathogenic bacteria isolated from diseased mulberry roots were investigated in a polyphasic taxonomic study. Comparative 16S rRNA gene sequence analysis combined with rpoB gene sequence analysis allocated strains R18-2(T) and R3-3 to the genus Enterobacter, with Enterobacter asburiae, E. amnigenus, E. cancerogenus, E. cloacae subsp. cloacae, E. cloacae subsp. dissolvens and E. nimipressuralis as their closest relatives. Cells of the isolates were Gram-negative, facultatively anaerobic rods, 0.3-1.0 µm wide and 0.8-2.0 µm long, with peritrichous flagella, showing a DNA G+C content of 55.1 ± 0.5 mol%. Calculation of a similarity index based on phenotypic features and fatty acid methyl ester (FAME) analysis suggested that these isolates are members of E. cancerogenus or E. asburiae or a closely related species. Biochemical data revealed that the isolates could be differentiated from their nearest neighbours by the presence of lysine decarboxylase activity and their ability to utilize d-arabitol. DNA-DNA relatedness also distinguished the two isolates from phylogenetically closely related Enterobacter strains. Based on these data, it is proposed that the isolates represent a novel species of the genus Enterobacter, named Enterobacter mori sp. nov. The type strain is R18-2(T) ( = CGMCC 1.10322(T) = LMG 25706(T)).

Phylogenetic analysis of the genera Proteus, Morganella and Providencia by comparison of rpoB gene sequences of type and clinical strains suggests the reclassification of Proteus myxofaciens in a new genus, Cosenzaea gen. nov., as Cosenzaea myxofaciens comb. nov

Phylogenetic analysis of partial rpoB gene sequences of type and clinical strains belonging to different 16S rRNA gene-fingerprinting ribogroups within 11 species of enterobacteria of the genera Proteus, Morganella and Providencia was performed and allowed the definition of rpoB clades, supported by high bootstrap values and confirmed by ≥2.5 % nucleotide divergence. None of the resulting clades included strains belonging to different species and the majority of the species were confirmed as discrete and homogeneous. However, more than one distinct rpoB clade could be defined among strains belonging to the species Proteus vulgaris (two clades), Providencia alcalifaciens (two clades) and Providencia rettgeri (three clades), suggesting that some strains represent novel species according to the genotypes outlined by rpoB gene sequence analysis. Percentage differences between the rpoB gene sequence of the type strain of Proteus myxofaciens and other members of the same genus (17.3-18.9 %) were similar to those calculated amongst strains of the genus Providencia (16.4-18.7 %), suggesting a genetic distance at the genus-level between Proteus myxofaciens and the rest of the Proteus-Providencia group. Proteus myxofaciens therefore represents a member of a new genus, for which the name Cosenzaea gen. nov., is proposed.

Degradation of hexadecane by Enterobacter cloacae strain TU that secretes an exopolysaccharide as a bioemulsifier

A Gram-negative rod-shaped bacterium, previously shown to utilize alkanes and polycyclic aromatic hydrocarbons (PAHs), was identified as Enterobacter cloacae (GenBank accession number, GQ426323) by 16S rRNA sequence analysis and was designated as strain TU. During growing on n-hexadecane as the sole carbon source, the strain TU extracellularly released an exopolysaccharide (EPS) exhibiting bioemulsifying activity into the surrounding medium. The EPS was found to be composed of glucose and galactose with molecular weight of 12.4+/-0.4 kDa. The structure of the EPS was postulated according to by 1D/2D NMR, as follows: -D-Glcp-(1 --> 3)-alpha-d-GlcpAc-(1 --> 3)-alpha-D-Galp-(1 --> 4)-alpha-D-Galp-(1 -->. While an enhanced emulsification and aqueous partitioning of n-hexadecane was displayed as functions of the EPS concentration, the EPS neutralized the zeta potential of E. cloacae TU cell and elevated the surface hydrophobicity of the cells, as determined by the microorganisms adhering to hydrocarbon assay (MATH). This was found to favor the bioavailability of n-hexadecane when it served as the sole carbon source for E. cloacae TU and thereby contributed to the accelerated degradation of this hydrocarbon.

Enterobacter spp.: a new evidence causing bacterial wilt on mulberry

Thirty-six pathogenetic bacterial strains were isolated from wilted mulberry plants in Hangzhou, Zhejiang province of China. The six representative strains were confirmed to be involved in more than one Enterobacter species by common bacteriological test, electron microscope observation, hypersensitive reaction, Koch's postulates, physiological and biochemical test, biology, fatty acid methyl esters analysis (FAMEs), enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR), 16s rRNA sequences analysis, and comparative analysis with 7 type strains and 3 reference strains. This is the first report on mulberry disease caused by Enterobacter spp. in the world providing new evidence on induction of the plant disease in this genus. The results are not only important in the mulberry disease management but also have significant scientific value for further studies of opportunistic human pathogens and environmental strains in Enterobacter.

Evolution in quantum leaps: multiple combinatorial transfers of HPI and other genetic modules in Enterobacteriaceae

Horizontal gene transfer is a key step in the evolution of Enterobacteriaceae. By acquiring virulence determinants of foreign origin, commensals can evolve into pathogens. In Enterobacteriaceae, horizontal transfer of these virulence determinants is largely dependent on transfer by plasmids, phages, genomic islands (GIs) and genomic modules (GMs). The High Pathogenicity Island (HPI) is a GI encoding virulence genes that can be transferred between different Enterobacteriaceae. We investigated the HPI because it was present in an Enterobacter hormaechei outbreak strain (EHOS). Genome sequence analysis showed that the EHOS contained an integration site for mobile elements and harbored two GIs and three putative GMs, including a new variant of the HPI (HPI-ICEEh1). We demonstrate, for the first time, that combinatorial transfers of GIs and GMs between Enterobacter cloacae complex isolates must have occurred. Furthermore, the excision and circularization of several combinations of the GIs and GMs was demonstrated. Because of its flexibility, the multiple integration site of mobile DNA can be considered an integration hotspot (IHS) that increases the genomic plasticity of the bacterium. Multiple combinatorial transfers of diverse combinations of the HPI and other genomic elements among Enterobacteriaceae may accelerate the generation of new pathogenic strains.

Mangrovibacter plantisponsor gen. nov., sp. nov., a nitrogen-fixing bacterium isolated from a mangrove-associated wild rice (Porteresia coarctata Tateoka)

A facultatively anaerobic, nitrogen-fixing bacterium, strain MSSRF40T, was isolated from roots of mangrove-associated wild rice (Porteresia coarctata Tateoka). On the basis of 16S rRNA gene sequence similarities, strain MSSRF40T was shown to belong to the family Enterobacteriaceae, most closely related to Cronobacter muytjensii E603T (97.2 % sequence similarity), Enterobacter cloacae subsp. dissolvens LMG 2683T (97.1 %), E. radicincitans D5/23T (97.1 %) and E. ludwigii EN-119T (97.0 %). Sequence analysis of rpoB, gyrB and hsp60 genes showed that strain MSSRF40T had relatively low sequence similarity (<91, <84 and <90 %) to recognized species of different genera of the family Enterobacteriaceae and formed an independent phyletic lineage in all phylogenetic analyses using the 16S rRNA, rpoB, gyrB and hsp60 genes, clearly indicating that strain MSSRF40T could not be affiliated to any of the recognized genera within the family Enterobacteriaceae. The dominant cellular fatty acids were C16 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH and C18 : 1 ω7c, similar to those of other members of the Enterobacteriaceae. The DNA G+C content was 50.1 mol%. Phylogenetic distinctiveness and phenotypic differences from its phylogenetic neighbours indicated that strain MSSRF40T represents a novel species and genus within the family Enterobacteriaceae, for which the name Mangrovibacter plantisponsor gen. nov., sp. nov. is proposed. The type strain of Mangrovibacter plantisponsor is strain MSSRF40T (=LMG 24236T =DSM 19579T).

[Enterobacter sakazakii in powdered infant food formulas]

Species of the Cronobacter genus ("Enterobacter sakazakii" s. l.) are emergent food-borne pathogens that can cause rare but severe neonatal meningitis, bacteriaemia, and necrotizing enterocolitis. Preterm, low-birth-weight, and immuno-compromised infants exposed to these bacterial species are at particular risk. Over the last 50 years, the literature has reported, mainly in newborn children, more than one hundred cases of infection due to these pathogens. The objective of this review was to synthesize the recent advances in knowledge of species of the Cronobacter genus, in particular with regards to taxonomy, physiology, pathogenicity, clinical cases, the methods for detection, isolation, and characterization, and their presence in powdered formulae for infants and young children, which were identified as the main infection vector. Researchers and international public health authorities have explored the ways contamination occur to better control the risks of pathogen development. Appropriate analysis and control measures were implemented in areas processing powdered formulae for infants and young children, and caregivers and families were informed to undertake good hygienic practices.

Specific distribution within the Enterobacter cloacae complex of strains isolated from infected orthopedic implants

Bacteria belonging to the Enterobacter genus are frequently isolated from clinical samples but are unusual causative agents of orthopedic implant infections. Twelve genetic clusters (clusters I to XII) and one sequence crowd (sequence crowd xiii) can be distinguished within the Enterobacter cloacae nomenspecies on the basis of hsp60 sequence analysis, and until now, none of these clusters could be specifically associated with a disease. In order to investigate if specific genetic clusters would be involved in infections of orthopedic material, two series of bacterial clinical isolates identified as E. cloacae by routine phenotypic identification methods were collected either from infected orthopedic implants (n = 21) or from randomly selected samples of diverse anatomical origins (control; n = 52). Analysis of the hsp60 gene showed that genetic clusters III, VI, and VIII were the most frequent genetic clusters detected in the control group, whereas cluster III was poorly represented among the orthopedic implant isolates (P = 0.006). On the other hand, E. hormaechei (clusters VI and VIII), but not cluster III, is predominantly associated with infections of orthopedic implants and, more specifically, with infected material in the hip (P = 0.019). These results support the hypothesis that, among the isolates within the E. cloacae complex, E. hormaechei and hsp60 gene sequencing-based cluster III are involved in pathogenesis in different ways and highlight the need for more accurate routine Enterobacter identification methods.

The rpoB gene as a tool for clinical microbiologists

The rpoB gene, encoding the beta-subunit of RNA polymerase, has emerged as a core gene candidate for phylogenetic analyses and identification of bacteria, especially when studying closely related isolates. Together with the 16S rRNA gene, rpoB has helped to delineate new bacterial species and refine bacterial community analysis, as well as enabling the monitoring of rifampicin resistance-conferring mutations. Sequencing of rpoB enables efficient estimation of bacterial G+C% content, DNA-DNA hybridization value and average nucleotide identity (percentage of the total genomic sequence shared between two strains) when taxonomic relationships have been firmly established. New identification tools targeting a rpoB gene fragment located between positions 2300 and 3300 have been developed recently. Therefore, inclusion of the rpoB gene sequence would be useful when describing new bacterial species.

Genomic diversity within the Enterobacter cloacae complex

Background

Isolates of the Enterobacter cloacae complex have been increasingly isolated as nosocomial pathogens, but phenotypic identification of the E. cloacae complex is unreliable and irreproducible. Identification of species based on currently available genotyping tools is already superior to phenotypic identification, but the taxonomy of isolates belonging to this complex is cumbersome.

Methodology/Principal Findings

This study shows that multilocus sequence analysis and comparative genomic hybridization based on a mixed genome array is a powerful method for studying species assignment within the E. cloacae complex. The E. cloacae complex is shown to be evolutionarily divided into two clades that are genetically distinct from each other. The younger first clade is genetically more homogenous, contains the Enterobacter hormaechei species and is the most frequently cultured Enterobacter species in hospitals. The second and older clade consists of several (sub)species that are genetically more heterogonous. Genetic markers were identified that could discriminate between the two clades and cluster 1.

Conclusions/Significance

Based on genomic differences it is concluded that some previously defined (clonal and heterogenic) (sub)species of the E. cloacae complex have to be redefined because of disagreements with known or proposed nomenclature. However, further improved identification of the redefined species will be possible based on novel markers presented here.

Phenotypic and genetic analysis of Enterobacter spp. from a Brazilian oligotrophic freshwater lake

We characterized a population of Enterobacter spp. of the Enterobacter cloacae complex isolated from an oligotrophic lake; most isolates were identified as E. cloacae. Fingerprinting polymerase chain reaction (PCR), along with morphological, biochemical, physiological, and plasmid profiles analyses, including antimicrobial susceptibility testing, were performed on 22 environmental isolates. Misidentification occurred when using the API 20E identification system. Analysis of 16S rDNA sequences confirmed the close relatedness between species of the E. cloacae complex. The tDNA PCR allowed the differentiation and identification of the E. cloacae isolates. Evaluation of genetic diversity by 16S rDNA sequence, tDNA, internal transcribed spacers, and enterobacterial repetitive intergenic concensus profiles revealed nearly identical isolates, although they exhibited different physiological and antimicrobial resistance profiles. Among the Enterobacter isolates, 96% were resistant to at least one antimicrobial; multiple resistance was also found at a high frequency (86%). The antimicrobials against which resistance was found most frequently were beta-lactams, chloramphenicol, and streptomycin. Plasmids were found in 21 of the 22 Enterobacter isolates. This confirms the conception that antibiotic resistance can occur in oligotrophic freshwater lake bacteria, which has important implications for public health.

Empreinte moléculaire des communautés bactériennes et hétérogénéité intraspécifique de l'ADNr 16S: est-il raisonnable d'occulter le problème?

Molecular fingerprinting methods are currently used to study microbial communities by culture independent approaches. They are proposed as identification tool owing to the availability of rapid automated methods. The 16S rRNA gene (16S rDNA) is an efficient marker for bacterial identification and microbial communities analysis. However, the 16S rDNA polymorphism among strains of the same species is an underestimated pitfall of the fingerprinting approaches.

AIM OF THE STUDY

We studied the 16S rDNA variability among strains of three bacterial species of medical interest.

MATERIAL AND METHODS

Total DNA was extracted from clinical isolates of Pseudomonas aeruginosa (N=20), Clostridium difficile (N=20) and Enterobacter cloacae (N=14). The Polymerase Chain Reaction (PCR) products obtained with consensus primers flanking the 16S rDNA variable regions V3 and V6-V7-V8 were separated by Temporal Temperature Gradient gel Electrophoresis (TTGE). DNA extracted from TTGE bands were sequenced and analysed.

RESULTS

All the isolates of P. aeruginosa and of C. difficile displayed one single TTGE band with constant migration distances suggesting that there was no 16S rDNA polymorphism among strains in these two species. Oppositely, the isolates of E. cloacae gave complex TTGE patterns formed by multiple bands with variable migration distances. These patterns corresponded to 16S rRNA genes variable in a single genome as well as among strains of the species.

CONCLUSION

Intra-species and/or intragenomic variability of 16S rDNA should be taken into account for pertinent interpretation of molecular fingerprint. For this purpose, a comprehensive description of the polymorphism of this marker is necessary.

A new method to extract dental pulp DNA: application to universal detection of bacteria

Background

Dental pulp is used for PCR-based detection of DNA derived from host and bacteremic microorganims. Current protocols require odontology expertise for proper recovery of the dental pulp. Dental pulp specimen exposed to laboratory environment yields contaminants detected using universal 16S rDNA-based detection of bacteria.

Methodology/Principal Findings

We developed a new protocol by encasing decontaminated tooth into sterile resin, extracting DNA into the dental pulp chamber itself and decontaminating PCR reagents by filtration and double restriction enzyme digestion. Application to 16S rDNA-based detection of bacteria in 144 teeth collected in 86 healthy people yielded a unique sequence in only 14 teeth (9.7%) from 12 individuals (14%). Each individual yielded a unique 16S rDNA sequence in 1–2 teeth per individual. Negative controls remained negative. Bacterial identifications were all confirmed by amplification and sequencing of specific rpoB sequence.

Conclusions/Significance

The new protocol prevented laboratory contamination of the dental pulp. It allowed the detection of bacteria responsible for dental pulp colonization from blood and periodontal tissue. Only 10% such samples contained 16S rDNA. It provides a new tool for the retrospective diagnostic of bacteremia by allowing the universal detection of bacterial DNA in animal and human, contemporary or ancient tooth. It could be further applied to identification of host DNA in forensic medicine and anthropology.

Enterobacter colonisation in newborn infants: predictors, follow-up and implications for infection control

Outbreaks with Enterobacter spp. have been described frequently in neonatal intensive care units (NICUs). This study investigated the factors that determine whether a neonate becomes colonised with Enterobacter spp., how long colonisation continues and whether the termination of isolation measures leads to spread of the organism. Neonates transferred from the NICUs of tertiary care hospitals were screened for the presence of Enterobacter spp. and any potential predictors for colonisation recorded. Those infected were monitored during their hospital stay and colonised neonates were screened every month for six months. Isolation infection control precautions were lifted and all neonates were screened for the presence of Enterobacter spp. six and 12 months later. Fifteen colonised neonates and 33 non-colonised controls were identified for study. Multivariate analysis showed that antibiotic therapy for more than three days and an Apgar score of <8 after 1 min were independently associated with Enterobacter spp. colonisation. Molecular typing using single-enzyme amplified-fragment length polymorphism (seAFLP) analysis revealed 22 different seAFLP genotypes. Three infants remained colonised with the same Enterobacter genotype after discharge; however, most neonates lost their strain or became colonised with another genotype. Lifting infection control measures for neonates colonised with Enterobacter spp. in a neonatal ward did not lead to increased incidence of colonisation and none of the infants became infected. Isolating neonates with susceptible Enterobacter spp. was not found to be necessary.

Molecular identification of coliform bacteria isolated from drinking water reservoirs with traditional methods and the Colilert-18 system

The accuracy of a traditional method (lactose utilization with acid and gas production) for the detection of coliform bacteria and E. coli was tested in comparison with method ISO 9308-1 (based on acid formation from lactose) and the Colilert-18 system (detection of beta-galactosidase). A total of 345 isolates were identified after isolation from water samples using API 20E strips. The Colilert-18 led to the highest number of positive findings (95% of the isolates were assigned to coliforms), whereas the ISO-9308-1 method resulted only in 29% coliform findings. With the traditional method only 15% were rated positive. Most of the isolates were identified by the API 20E system as Enterobacter spp. (species of the Enterobacter cloacae complex), Serratia spp., Citrobacter spp.and Klebsiella spp.; but species identification remained vague in several cases. A more detailed identification of 126 pure cultures by using 16S rRNA gene sequence analysis and analysis of the hsp60 gene resulted in the identification of Enterobacter nimipressuralis, E. amnigenus, E. asburiae, E. hormaechei, and Serratia fonticola as predominat coliforms. These species are beta-galactosidase positive, but show acid formation from lactose often after a prolonged incubation time. They are often not of fecal origin and may interfere with the ability to accurately detect coliforms of fecal origin.

Molecular approaches: advantages and artifacts in assessing bacterial diversity

Bacteria account for a major proportion of Earth's biological diversity. They play essential roles in quite diverse environments and there has been an increasing interest in bacterial biodiversity. Research using novel and efficient tools to identify and characterize bacterial communities has been the key for elucidating biological activities with potential for industrial application. The current approach used for defining bacterial species is based on phenotypic and genomic properties. Traditional and novel DNA-based molecular methods are improving our knowledge of bacterial diversity in nature. Advances in molecular biology have been important for studies of diversity, considerably improving our knowledge of morphological, physiological, and ecological features of bacterial taxa. DNA-DNA hybridization, which has been used for many years, is still considered the golden standard for bacteria species identification. PCR-based methods investigating 16S rRNA gene sequences, and other approaches, such as the metagenome, have been used to study the physiology and diversity of bacteria and to identify novel genes with potential pharmaceutical and other biotechnological applications. We examined the advantages and limitations of molecular methods currently used to analyze bacterial diversity; these are mainly based on the 16S rRNA gene. These methods have allowed us to examine microorganisms that cannot be cultivated by routine methods and have also been useful for phylogenetic studies. We also considered the importance of improvements in microbe culture techniques and how we can combine different methods to allow a more appropriate assessment of bacterial diversity and to determine their real potential for industrial applications.

Type II topoisomerase mutations in clinical isolates of Enterobacter cloacae and other enterobacterial species harbouring the qnrA gene

The qnr genes are transferable genes that confer low-level quinolone resistance by protection of topoisomerase. The occurrence of mutations in DNA gyrase (gyrA, gyrB) and topoisomerase IV (parC, parE) genes in strains harbouring qnr was investigated in 28 qnrA-positive clinical isolates, among which 7 strains also harboured qnrS. Topoisomerase mutations were found in 25 (89%) of the 28 strains, with at least two mutations (gyrA and parC) in 13 strains and one mutation in 12 strains. Isolates of the Enterobacter cloacae complex were compared with reference strains of the new Enterobacter species. gyrA mutations were found at position 83 (Ser or Thr for Ile, Tyr, Leu or Phe depending on the species), and new gyrB mutations were described (S463A, S464F). qnrA had an additive effect of a 10-fold increase in the minimum inhibitory concentration (MIC) whatever the number of topoisomerase mutations, and qnrS was additive to qnrA with a further 2- to 10-fold increase in the MIC. Comparison of MICs with susceptibility breakpoints showed that strains combining qnrA and topoisomerase mutations were resistant to fluoroquinolones, but the three strains lacking a topoisomerase mutation were susceptible using ciprofloxacin and levofloxacin but not using nalidixic acid or moxifloxacin testing.

The biochemical differentiation of Enterobacter sakazakii genotypes

BACKGROUND

Enterobacter sakazakii is an emergent pathogen that has been associated with neonatal infections through contaminated powdered infant milk formula. The species was defined by Farmer et al. (1980) who described 15 biogroups according to the biochemical characterization of 57 strains. This present study compares genotypes (DNA cluster groups based on partial 16S rDNA sequence analysis) with the biochemical traits for 189 E. sakazakii strains.

RESULTS

Analysis of partial 16S rDNA sequences gave 4 well defined phylogenetic groups. Cluster group 1 was composed of the majority of strains (170/189) and included Biogroups 1-5, 7-9, 11, 13 and 14. Cluster 3 corresponded with Biogroup 15 and cluster 4 with Biogroups 6, 10 and 12. Cluster group 2 comprised a new Biogroup 16. For the isolates in this study, the four DNA cluster groups can be distinguished using the inositol, dulcitol and indole tests.

CONCLUSION

This study demonstrates an agreement between genotyping (partial 16S rDNA) and biotyping and describes a new biogroup of E. sakazakii.

Two-center collaborative evaluation of performance of the BD phoenix automated microbiology system for identification and antimicrobial susceptibility testing of gram-negative bacteria

The performance of the BD Phoenix Automated Microbiology System (BD Diagnostic Systems, Sparks, MD) was assessed for identification (ID) and antimicrobial susceptibility testing (AST) of the majority of clinically encountered bacterial isolates in a European collaborative two-center trial. A total of 494 bacterial isolates including various species of the Enterobacteriaceae and 110 nonfermentative gram-negative bacteria were investigated: of these, 385 were single patient isolates, and 109 were challenge strains tested at one center. The performance of the Phoenix extended-spectrum beta-lactamase (ESBL) test was also evaluated for 203 strains of Escherichia coli, Klebsiella pneumoniae, and Klebsiella oxytoca included in the study. Forty-two antimicrobial drugs were tested, including members of the following drug classes: aminoglycosides, beta-lactam antibiotics, beta-lactam/beta-lactamase inhibitors, carbapenems, cephems, monobactams, folate antagonists, quinolones, and others. Phoenix system ID results were compared to those of the laboratories' routine ID systems (API 20E and API CHE, ATB ID32E, ID32GN, and VITEK 2 [bioMérieux, Marcy l'Etoile, France]); Phoenix AST results were compared to those of frozen standard broth microdilution (SBM) panels according to NCCLS (now CLSI) guidelines (NCCLS document M100-S9, approved standard M7-A4). Discrepant results were repeated in duplicate. Concordant IDs of 98.4 and 99.1% were observed for the Enterobacteriaceae and the nonfermentative group, respectively. For AST results, the overall essential agreement was 94.2%; the category agreement was 97.3%; and the very major error rate, major error rate, and minor error rate were 1.6, 0.6, and 1.9%, respectively. In terms of ESBL detection, Phoenix results were 98.5% concordant with those of the reference system, with 98.0% sensitivity and 98.7% specificity. In conclusion, the Phoenix ID results showed high agreement with results of the systems to which they were being compared: the AST performance was highly equivalent to that of the SBM reference method, and the system proved to be very accurate for the detection of ESBL producers.

Phylogenetic analysis of enteric species of the family Enterobacteriaceae using the oriC-locus

Phylogenetic analysis of 38 enteric species belonging to the Enterobacteraceae family was carried out using the non-coding locus oriC, the chromosomal replication origin. The oriC loci were amplified with conserved oligonucleotides and the PCR fragments were sequenced directly. The results establish a phylogenetic tree for the classification of different species of the genera Escherichia, Shigella, Salmonella, Enterobacter, Citrobacter, Klebsiella, Raoultella, Kluyvera, Cedecea and Buttiauxella. Functional important protein-binding sites located in oriC are well conserved throughout the enteric group. More over, due to a high overall divergence value phylogenetic trees were robust and well supported by bootstrap analysis. In comparison with 16S rDNA analysis, the oriC sequences indicated a greater evolutionary divergence for bacteria. We propose that the oriC locus might be a suitable phylogenetic marker for the identification and classification of bacteria, in particular for closely related species.

Direct identification of bacteria in clinical respiratory samples using fluorescent amplicon length analysis of 16S–23S rRNA spacer-region

We describe the development and application of a rapid and universal molecular technique for direct identification of multiple bacteria in clinical samples. Amplification of the 16S-23S rRNA spacer-region using universal primers led to fragment patterns distinct for different bacterial species and that were analyzed with fluorescent amplicon length analysis (FALA). 136 pure cultures of clinical isolates and 20 culture collection strains belonging to 22 different medically important species were used to create a primary database of fragments with sizes between 100 and 1000 bp. Subsequently, 127 respiratory samples were analyzed with culture-based techniques and via FALA of the 16S-23S rRNA spacer-region. Two DNA extraction methods were evaluated: Instagene (FALA-I) and Fastprept (FALA-P). Of the 127 samples, 26 culture-negative samples were also negative with FALA-P. Of 18 samples with growth of commensal oral flora, 10 gave a mixed oral flora pattern with FALA-P and 8 gave a negative result. For 54 samples with growth of a single bacterial species, FALA-P gave an identical result for 46. For 29 samples with growth of more than one bacterial species, identical results were obtained in 19 samples. False-negative results with FALA-P were mostly due to paucity (less than 10(3) CFU/ml) of bacteria (12 out of 18 false-negatives) or difficulties with homogenization of viscous samples (6 out of 18 false-negatives).With regard to identification of all significant pathogens of clinical samples tested, the sensitivity of FALA-P was 77% and its specificity was 100%. With FALA-I, the number of false-negative results was higher than with FALA-P due to less efficient extraction of DNA, particularly with Staphylococcal species. FALA-P allows rapid and direct identification of multiple species directly from clinical samples; pauci-cellular samples may give false-negative results.

Rapid identification of Enterobacteriaceae by sequencing DNA gyrase subunit B encoding gene

Real-time polymerase chain reaction and sequencing were used to characterize a 506-bp-long DNA fragment internal to the gyrB gene (gyrBint). The sequences obtained from 32 Enterobacteriaceae-type strains and those available in the Genbank nucleotide sequence database (n = 24) were used as a database to identify 240 clinical enterobacteria isolates. Sequence analysis of the gyrBint fragment of 240 strains showed that gyrBint constitutes a discriminative target sequence to differentiate between Enterobacteriaceae species. Comparison of these identifications with those obtained by phenotypic methods (Vitek 1 system and/or Rapid ID 32E; bioMérieux, Marcy l'Etoile, France) revealed discrepancies essentially with genera Citrobacter and Enterobacter. Most of the strains identified as Enterobacter cloacae by phenotypic methods were identified as Enterobacter hormaechei strains by gyrBint sequencing. The direct sequencing of gyrBint would be useful as a complementary tool in the identification of clinical Enterobacteriaceae isolates.

Prevalence of extended-spectrum β-lactamases in isolates of the Enterobacter cloacae complex from German hospitals

In 2002, 119 isolates of the Enterobacter cloacae complex were collected randomly from 11 German laboratories nationwide. Antibiotic susceptibilities were tested by disk-diffusion tests according to CLSI guidelines, and MICs were determined using Etests. PCRs were performed to amplify all TEM and SHV, and most CTX-M and OXA beta-lactamase genes. PCR products were sequenced to identify the precise extended spectrum beta-lactamase (ESBL) types. Isoelectric focusing (IEF) and PM/PML Etests were used to confirm production of the respective ESBLs. According to susceptibility tests and CLSI criteria, 49 (40%) isolates were resistant to extended-spectrum cephalosporins. Seven (5.8%) isolates were positive in at least one of the PCR assays. Sequencing identified production of TEM-1 beta-lactamase genes by three (2.9%) isolates, and ESBL genes of the CTX-M and SHV beta-lactamase families by five (4.2%) isolates. IEF confirmed the production of beta-lactamases in the expected pI ranges of the respective ESBLs, and four of the five ESBL-producers were detected using the PM/PML Etest. All ESBL-producing isolates showed co-resistance to sulphonamides.

Specificity of enterobacterial repetitive intergenic consensus and repetitive extragenic palindromic polymerase chain reaction for the detection of clonality within the Enterobacter cloacae complex

An increasing number of clonal outbreaks caused by members of the E. cloacae complex is being reported. For the detection of clonality, pulsed-field gel electrophoresis (PFGE) is considered the golden standard, but PCR-based methods are cheaper, easier to perform, and provide faster results. One hundred ninety-five isolates of the E. cloacae complex isolated at the university hospital Grosshadern, Munich, Germany, were assigned to their respective genetic cluster by partial hsp60 sequencing. All study isolates belonging to genetic clusters III and VI were selected to evaluate the specificity of the enterobacterial repetitive intergenic consensus (ERIC) and repetitive extragenic palindromic (REP) polymerase chain reaction (PCR) for the identification of clonal isolates belonging to the E. cloacae complex. For these 56 isolates, PFGE was performed, yielding 3 pairs of isolates with indistinguishable patterns. ERIC PCR resulted in 7 groups with identical patterns, together encompassing 49 study isolates. Comparing the ERIC PCR with the PFGE, a specificity of 14% considering the detection of "clonal" isolates was calculated. In this respect, REP PCR performed much better, yielding a specificity of 90%. An unweighted pair-group method with arithmetic averages tree based on ERIC PCR patterns allowed an accurate classification of the isolates to the respective genovars, suggesting that the ERIC PCR differentiates between genovars rather than between strains. In contrast, REP PCR differentiates better on the strain level. A proposed diagnostic system for the detection of subsumed outbreak strains of the E. cloacae complex is presented. It is based on an initial REP PCR, which should be confirmed by PFGE in cases of identical patterns, whereas ERIC PCR does not seem to be useful for the detection of outbreak strains when dealing with isolates of the E. cloacae complex.

Nosocomial urosepsis caused by Enterobacter kobei with aberrant phenotype

Enterobacter kobei is the species of the Enterobacter cloacae complex, which is phenotypically most closely related to the species E. cloacae. This is the first report of infection caused by a new biotype of E. kobei. A patient with a history of urinary bladder operation developed a urosepsis with an Enterobacter isolate displaying the E. cloacae phenotype. The isolate was classified to the species E. kobei by sequence analysis of the 16S-rDNA, 4 protein-coding genes and enterobacterial repetitive intergenic consensus (ERIC)-cluster analysis. E. kobei was originally described to be Voges-Proskauer (VP) negative. However, the isolates of the present case were VP-positive. After analyzing 120 biochemical tests included in the API20E and the Biotype 100 systems, 4 biochemical tests were identified potentially differentiating this new biotype from E. cloacae.

Enterobacter hormaechei subsp. oharae subsp. nov., E. hormaechei subsp. hormaechei comb. nov., and E. hormaechei subsp. steigerwaltii subsp. nov., three new subspecies of clinical importance

Six species and six additional genovars are combined within the so-called Enterobacter cloacae complex, with one of them being the species Enterobacter hormaechei. In a recent population genetic study, two genetic clusters were found in close phylogenetic proximity to the genetic cluster of E. hormaechei. In order to prove the hypothesis that these three genetic clusters belong to the same species, we performed cross-hybridization experiments in microplates with DNAs of representatives of each genetic cluster. The close phylogenetic relationship among the clusters was reflected by their relatively low deltaT(m) values, ranging from 0.3 to 4.8, confirming the hypothesis that the clusters are parts of the same species. These clusters can be distinguished from the other species of the E. cloacae complex, which have deltaT(m) values of 5.6 to 10.3. Forty-eight E. hormaechei strains from the different genetic clusters were phenotypically characterized with 129 biochemical tests. In this way, E. hormaechei could be differentiated from the other species of the E. cloacae complex because it tests negative in the 3-hydroxy-butyrate test. The three genetic clusters of E. hormaechei could also be differentiated from each other by using phenotypic tests. Hence, we propose three new subspecies of E. hormaechei corresponding to genetic clusters VI, VII, and VIII of the E. cloacae complex. E. hormaechei subsp. hormaechei comb. nov. corresponds to the original species description, as it gives negative results for the adonitol, d-arabitol, d-sorbitol, and d-melibiose tests and a positive result for the dulcitol test. E. hormaechei subsp. oharae subsp. nov. gives negative results for the dulcitol, adonitol, and d-arabitol tests and positive results for the d-sorbitol and d-melibiose tests. E. hormaechei subsp. steigerwaltii subsp. nov. gives a negative result for the dulcitol test and positive results for the adonitol, d-arabitol, d-sorbitol, and d-melibiose tests. Among the members of the E. cloacae complex, E. hormaechei seems to be the species most frequently recovered from clinical specimens.

Reassignment of enterobacter dissolvens to Enterobacter cloacae as E. cloacae subspecies dissolvens comb. nov. and emended description of Enterobacter asburiae and Enterobacter kobei

The taxonomic position of Enterobacter dissolvens was re-evaluated based on the analysis of the type strain ATCC 23373T and three clinical isolates. The strains were assigned to the genetic cluster of the species by phylogenetic sequence analysis in the frame of a recent population genetic study. The relatedness of E. dissolves to the other species of the E. cloacae complex was analyzed by DNA-DNA hybridization studies based on melting profiles in microplates. The genetic cluster of E. dissolvens fell into the same DNA-relatedness group like E. cloacae with mean deltaTm-values of 3.9 degrees C confirming the hybridization results of three former studies. Phenotypic analysis of the E. cloacae and E. dissolvens strains, respectively, based on 115 biochemical reactions yielded the esculin test as the only one differentiating between them by being positive for E. dissolvens and negative for E. cloacae strains. The name E. cloacae subsp. dissolvens comb. nov. is proposed for the group of organisms formerly referred to as E. dissolvens, and the name E. cloacae subsp. cloacae comb. nov. for the group of organisms formerly referred to as E. cloacae. The species descriptions of Enterobacter kobei and Enterobacter asburiae were emended based on the data collected on 17 and 15 strains, respectively. The strains were assigned to the respective species by a combination of phylogenetic sequence analyzes and DNA-DNA hybridizations. Phenotypic analyzes of 115 reactions gave detailed species profiles with new differentiating phenotypic properties.

Enterobacter radicincitans sp. nov., a plant growth promoting species of the family Enterobacteriaceae

A plant growth promoting bacterial isolate (D5/23T) from the phyllosphere of winter wheat, able to fix atmospheric nitrogen and to produce auxines and cytokinins was investigated in a polyphasic taxonomy approach. Phylogenetic analyses using the 16S rRNA gene sequence of the strain clearly indicated that the strain belonged to the family Enterobacteriaceae, most closely related to Enterobacter cloacae with 99.0% and Enterobacter dissolvens with 98.5% sequence similarity. Phylogenetic analysis derived from the sequence of the rpoB gene showed the highest sequence similarities to Enterobacter cowanii (93.0%) but supported the distinct position of strain D5/23T. The isolate produced a fatty acid pattern typical for members of the family Enterobacteriaceae. On the basis of the phylogenetic analyses, DNA-DNA hybridizations, and the unique physiological and biochemical characteristics, we propose that strain D5/23T represents a new species of the genus Enterobacter for which we propose the name Enterobacter radicincitans sp. nov.

Description of Enterobacter ludwigii sp. nov., a novel Enterobacter species of clinical relevance

A new species, Enterobacter ludwigii, is presented on the basis of the characteristics of 16 strains, which were isolated from clinical specimens. These bacteria form a distinct genetic cluster in phylogenetic analyses of the population structure of the Enterobacter cloacae complex. As determined by DNA-DNA cross-hybridization experiments in microplates, this genetic cluster can be delineated from the other species of the E. cloacae complex with deltaTm values equal to or above 5 degrees C with Enterobacter hormaechei being the closest relative. The bacteria are gram-negative, fermentative, motile rods with the general characteristics of the genus Enterobacter and the E. cloacae complex in particular. E. ludwigii can be differentiated from the other Enterobacter species by its growth on myo-inositol and 3-0-methyl-D-glucopyranose. The type strain is EN-119 (= DSM 16688T = CIP 108491T).

Detection and characterization of extended-spectrum β-lactamases among bloodstream isolates of Enterobacter spp. in Hong Kong, 2000–2002

OBJECTIVES

A total of 139 consecutive and non-duplicate bloodstream isolates of Enterobacter spp. collected from inpatients in Hong Kong during 2000-2002 were studied for production of extended-spectrum beta-lactamases (ESBLs).

METHODS

All isolates were evaluated by the modified double-disc synergy test (m-DDST), the combined disc method (CDM) and the three-dimensional (3D) test. The m-DDST and CDM were modified by the use of cefepime discs. beta-Lactamases were characterized by isoelectric focusing and PCR sequencing using specific primers.

RESULTS

ESBLs were identified in nine isolates (overall 6.5%), including seven of 39 (17.9%) Enterobacter hormaechei, one of 27 (3.7%) Enterobacter aerogenes and the only Enterobacter intermedius strain. The E. intermedius strain was positive only in the 3D test but not in the other two tests. The other eight strains were positive in all three tests. No ESBL was detected in the other species, including non-hormaechei members of the Enterobacter cloacae complex (n=61), Enterobacter agglomerans (n=7), Enterobacter gergoviae (n=4) and Enterobacter sakazakii (n=1). The ESBL content included five different CTX-M enzymes (CTX-M-9, CTX-M-13, CTX-M-14, CTX-M-24 and a novel CTX-M-2-like beta-lactamase), SHV-12 (n=2) and unidentifiable ESBLs with a pI of 7.7 or 7.9 in two strains. The seven ESBL-producing E. hormaechei were genotyped by pulsed-field gel electrophoresis and were found to be unrelated to each other. In three of the CTX-M-producing strains, ISEcp1-like elements, including promoters for the beta-lactamase gene, were found.

CONCLUSIONS

Our data underscore the diversity of CTX-M enzymes among Enterobacter spp. in Hong Kong.

Identification and phylogeny of Enterobacter sakazakii relative to Enterobacter and Citrobacter Species

The phylogenetic relationships of Enterobacter sakazakii strains were investigated using 16S ribosomal DNA (rDNA) and hsp60 sequencing. Each analysis distributed E. sakazakii strains among four clusters, indicating substantial taxonomic heterogeneity. The E. sakazakii type strain 16S rDNA sequence was 97.8% similar to that of Citrobacter koseri but 97.0% similar to that of Enterobacter cloacae.

Microbiological, epidemiological, and food safety aspects of Enterobacter sakazakii

Enterobacter sakazakii is considered to be an opportunistic pathogen and has been implicated in foodborne diseases causing meningitis or enteritis, especially in neonates and infants. The U.S FoodNet 2002 survey rate of invasive infections with this organism in infants under 1 year of age was 1 per 100,000 infants. Severity of the disease is a matter of concern. In a recent study on the occurrence of E. sakazakii in production environments from food (milk powder, chocolate, cereal, potato, and pasta) factories and households, this organism was isolated with varying frequency from nearly all environments examined, strongly indicating that it is widespread. Stationary phase E. sakazakii cells are remarkably resistant to osmotic and drying stresses compared with other species of the Enterobacteriacae. In this article, we review the literature on this organism with special respect to the information relevant for food safety.

Growth control of small-colony variants by genetic regulation of the hemin uptake system

Small-colony variants (SCVs) are slow-growing variants of human bacterial pathogens. They are associated with chronic persistent infections, and their biochemical identification and antimicrobial treatment are impaired by altered metabolic properties. To contribute to the understanding of SCV-mediated infections, we analyzed a clinical SCV isolate derived from a chronic prosthetic hip infection. A sequence analysis of housekeeping genes identified an Enterobacter hormaechei-like organism. The SCV phenotype, with growth as microcolonies, was caused by a block within the heme biosynthesis pathway through deletion of the hemB locus, as shown by hybridization and complementation experiments. At a low frequency, large-colony variants (LCVs) arose that were dependent on exogenous hemin. To investigate this phenomenon, we cloned and sequenced the 5.8-kb hemin uptake system, denoted ehu. Gene expression analysis indicated regulation of this locus in wild-type bacteria by the global iron regulator Fur. Inactivation of Fur in LCVs caused the derepression of ehu expression and facilitated bacterial growth. Genetic alterations of the fur locus in LCVs were identified as insertions of IS1A elements and point mutations. In contrast, SCVs could utilize exogenous hemin only in the absence of iron. Thus, we provide the first molecular characterization of the growth properties of a clinical SCV isolate, which may help to improve the diagnostic and therapeutic management of patients with chronic persistent infections.